Variant report

Variant	rs8179648
Chromosome Location	chr2:179377280-179377281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179377244..179379642-chr2:179381924..179384722,3	K562	blood:
2	chr2:179371835..179375204-chr2:179376533..179381203,4	K562	blood:
3	chr2:179364022..179368835-chr2:179377215..179381031,4	K562	blood:
4	chr2:179376615..179380238-chr2:179382485..179386647,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001238	0.80[JPT][hapmap]
rs10188593	0.85[CEU][hapmap]
rs10207436	0.95[JPT][hapmap]
rs10930831	0.95[JPT][hapmap]
rs11688081	0.91[YRI][hapmap]
rs12052983	0.95[JPT][hapmap]
rs12615347	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13382684	0.82[AMR][1000 genomes]
rs13411588	0.95[JPT][hapmap]
rs1559908	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1560221	0.85[JPT][hapmap]
rs16866334	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16866342	0.94[JPT][hapmap]
rs16866400	0.85[JPT][hapmap]
rs16866420	0.85[JPT][hapmap]
rs1863671	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1967327	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs1978580	0.95[JPT][hapmap]
rs2042996	0.90[JPT][hapmap]
rs2059691	0.80[JPT][hapmap]
rs2114582	0.90[JPT][hapmap]
rs2163009	0.85[JPT][hapmap]
rs2249737	0.80[JPT][hapmap]
rs2288320	0.91[ASW][hapmap];0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs2288322	0.95[JPT][hapmap]
rs2303536	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes]
rs2303537	0.95[JPT][hapmap]
rs2366751	0.85[JPT][hapmap]
rs33998881	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3731750	0.90[JPT][hapmap]
rs3731754	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3752689	0.95[JPT][hapmap]
rs3769866	0.95[JPT][hapmap];0.81[TSI][hapmap]
rs3813250	0.85[JPT][hapmap]
rs3829746	0.85[JPT][hapmap]
rs4019558	0.91[YRI][hapmap]
rs4404314	0.91[YRI][hapmap]
rs4894017	0.85[JPT][hapmap]
rs4894020	0.95[JPT][hapmap]
rs4894029	0.85[JPT][hapmap]
rs60488846	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6704545	0.95[JPT][hapmap]
rs6739142	0.95[JPT][hapmap]
rs6753709	0.95[JPT][hapmap]
rs7575643	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7577862	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7588593	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7589679	0.95[JPT][hapmap]
rs7598228	0.94[JPT][hapmap]
rs7600176	0.95[JPT][hapmap]
rs7602597	0.81[TSI][hapmap]
rs9288019	0.95[JPT][hapmap]
rs957875	0.90[JPT][hapmap]
rs967507	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9808377	0.85[JPT][hapmap]
rs9967820	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8179648	CHAD	trans	brain	seeQTL
rs8179648	TIMP4	trans	brain	seeQTL
rs8179648	EOMES	trans	brain	seeQTL
rs8179648	PLEKHA3	cis	lymphoblastoid	seeQTL
rs8179648	ZNF385B	cis	parietal	SCAN
rs8179648	BARHL1	trans	brain	seeQTL
rs8179648	FKBP7	cis	lymphoblastoid	seeQTL
rs8179648	PCP2	trans	brain	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179346400-179387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:179350400-179384400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:179359400-179382800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:179359600-179387600	Weak transcription	Right Ventricle	heart
5	chr2:179359600-179387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:179360600-179382400	Weak transcription	Gastric	stomach
7	chr2:179360600-179383200	Weak transcription	Pancreas	Pancrea
8	chr2:179360800-179383000	Weak transcription	Aorta	Aorta
9	chr2:179360800-179387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:179361000-179387800	Weak transcription	Spleen	Spleen
11	chr2:179361400-179387200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:179364600-179382800	Weak transcription	Thymus	Thymus
13	chr2:179365000-179383000	Weak transcription	Lung	lung
14	chr2:179365600-179387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:179366000-179387600	Weak transcription	Fetal Brain Male	brain
16	chr2:179366000-179387800	Weak transcription	Small Intestine	intestine
17	chr2:179367400-179383200	Weak transcription	NHLF	lung
18	chr2:179367600-179387600	Weak transcription	Fetal Kidney	kidney
19	chr2:179367800-179387600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:179368000-179378600	Weak transcription	NHEK	skin
21	chr2:179368000-179379600	Weak transcription	Left Ventricle	heart
22	chr2:179368000-179383000	Weak transcription	Ovary	ovary
23	chr2:179368200-179378800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:179368200-179378800	Weak transcription	HSMMtube	muscle
25	chr2:179368200-179379200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:179368200-179382400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:179368200-179387600	Weak transcription	Fetal Heart	heart
28	chr2:179368200-179387600	Weak transcription	Fetal Lung	lung
29	chr2:179368200-179387800	Weak transcription	Brain Substantia Nigra	brain
30	chr2:179368400-179383000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:179368400-179383400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:179368400-179387400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:179368400-179387600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:179368600-179378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:179368600-179381200	Weak transcription	Brain Anterior Caudate	brain
36	chr2:179368600-179382400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:179368600-179382600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:179368600-179383000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:179368600-179387400	Weak transcription	A549	lung
40	chr2:179368600-179387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:179368600-179387800	Weak transcription	Psoas Muscle	Psoas
42	chr2:179368800-179378400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:179369000-179378600	Weak transcription	HMEC	breast
44	chr2:179369000-179387400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:179369200-179378600	Weak transcription	NHDF-Ad	bronchial
46	chr2:179369200-179387400	Weak transcription	K562	blood
47	chr2:179369200-179387600	Weak transcription	HUVEC	blood vessel
48	chr2:179369600-179382200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:179369800-179378800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:179369800-179382400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links